Analysis of moss change
Wouter Van Landuyt, Hans Van Calster
2021-01-05
## Loading required package: assertthat##
## Attaching package: 'assertthat'## The following object is masked from 'package:tibble':
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## has_name## Loading required package: glue##
## Attaching package: 'glue'## The following object is masked from 'package:dplyr':
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## collapse## Loading required package: rlang## Warning: package 'rlang' was built under R version 4.0.3##
## Attaching package: 'rlang'## The following object is masked from 'package:assertthat':
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## has_name## The following objects are masked from 'package:purrr':
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## %@%, as_function, flatten, flatten_chr, flatten_dbl, flatten_int,
## flatten_lgl, flatten_raw, invoke, list_along, modify, prepend,
## splice##
## -- Column specification --------------------------------------------------------
## cols(
## id = col_double(),
## code = col_character(),
## naam_nederlands = col_character(),
## naam_wetenschappelijk = col_character(),
## taxn_vrs_key = col_character(),
## taxongroep = col_character(),
## usageKey = col_double(),
## scientificName = col_character(),
## rank = col_character(),
## order = col_character(),
## matchType = col_character(),
## phylum = col_character(),
## kingdom = col_character(),
## genus = col_character(),
## class = col_character(),
## confidence = col_double(),
## synonym = col_logical(),
## status = col_character(),
## family = col_character()
## )## i Using ',' as decimal and '.' as grouping mark. Use `read_delim()` for more control.##
## -- Column specification --------------------------------------------------------
## cols(
## substraat = col_character(),
## substrate = col_character()
## )Exploratory data analysis
- Anthocerotophyta = hornworth = hauwmossen
- Bryophyta = bryophytes = bladmossen
- Marchantiophyta = liverworths = levermossen
## `summarise()` ungrouping output (override with `.groups` argument)| phylum | n_obs | n_soorten | n_hokken |
|---|---|---|---|
| Anthocerotophyta | 218 | 4 | 123 |
| Bryophyta | 95349 | 410 | 796 |
| Marchantiophyta | 17462 | 109 | 727 |
## `summarise()` regrouping output by 'phylum' (override with `.groups` argument)## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Alternative Telfer method
Goed onderzocht = 40 of meer soorten in een uurhok per periode
Uurhok moet in beide perioden goed onderzocht zijn.
## Joining, by = "substraat"| phylum | substrate | number of species |
|---|---|---|
| Bryophyta | artificial stone | 84 |
| Bryophyta | bryophyte | 3 |
| Bryophyta | decaying vegetation | 21 |
| Bryophyta | decorticated wood | 48 |
| Bryophyta | epiphytic on living wood | 73 |
| Bryophyta | floating on water | 1 |
| Bryophyta | gravel or sand | 106 |
| Bryophyta | mineral soil | 210 |
| Bryophyta | peat | 46 |
| Bryophyta | rock, hard | 95 |
| Bryophyta | rock, soft | 38 |
| Bryophyta | soil on rock | 68 |
| Marchantiophyta | artificial stone | 9 |
| Marchantiophyta | bryophyte | 17 |
| Marchantiophyta | decaying vegetation | 18 |
| Marchantiophyta | decorticated wood | 16 |
| Marchantiophyta | epiphytic on living wood | 15 |
| Marchantiophyta | floating on water | 3 |
| Marchantiophyta | gravel or sand | 34 |
| Marchantiophyta | mineral soil | 67 |
| Marchantiophyta | peat | 30 |
| Marchantiophyta | rock, hard | 14 |
| Marchantiophyta | rock, soft | 14 |
| Marchantiophyta | soil on rock | 20 |
| phylum | ell_l | number of species |
|---|---|---|
| Bryophyta | 1 | 9 |
| Bryophyta | 2 | 19 |
| Bryophyta | 3 | 37 |
| Bryophyta | 4 | 86 |
| Bryophyta | 5 | 125 |
| Bryophyta | 6 | 188 |
| Bryophyta | 7 | 188 |
| Bryophyta | 8 | 126 |
| Bryophyta | 9 | 15 |
| Marchantiophyta | 1 | 1 |
| Marchantiophyta | 3 | 20 |
| Marchantiophyta | 4 | 51 |
| Marchantiophyta | 5 | 51 |
| Marchantiophyta | 6 | 60 |
| Marchantiophyta | 7 | 56 |
| Marchantiophyta | 8 | 18 |
| phylum | ell_r | number of species |
|---|---|---|
| Bryophyta | 1 | 10 |
| Bryophyta | 2 | 63 |
| Bryophyta | 3 | 88 |
| Bryophyta | 4 | 67 |
| Bryophyta | 5 | 95 |
| Bryophyta | 6 | 138 |
| Bryophyta | 7 | 214 |
| Bryophyta | 8 | 101 |
| Bryophyta | 9 | 17 |
| Marchantiophyta | 1 | 28 |
| Marchantiophyta | 2 | 60 |
| Marchantiophyta | 3 | 20 |
| Marchantiophyta | 4 | 52 |
| Marchantiophyta | 5 | 30 |
| Marchantiophyta | 6 | 38 |
| Marchantiophyta | 7 | 21 |
| Marchantiophyta | 8 | 6 |
| Marchantiophyta | 9 | 2 |
| phylum | ell_f | number of species |
|---|---|---|
| Bryophyta | 1 | 12 |
| Bryophyta | 2 | 12 |
| Bryophyta | 3 | 61 |
| Bryophyta | 4 | 152 |
| Bryophyta | 5 | 187 |
| Bryophyta | 6 | 176 |
| Bryophyta | 7 | 50 |
| Bryophyta | 8 | 69 |
| Bryophyta | 9 | 51 |
| Bryophyta | 10 | 14 |
| Bryophyta | 11 | 4 |
| Bryophyta | 12 | 5 |
| Marchantiophyta | 4 | 15 |
| Marchantiophyta | 5 | 51 |
| Marchantiophyta | 6 | 52 |
| Marchantiophyta | 7 | 50 |
| Marchantiophyta | 8 | 47 |
| Marchantiophyta | 9 | 32 |
| Marchantiophyta | 10 | 9 |
| Marchantiophyta | 11 | 1 |
| phylum | ell_n | number of species |
|---|---|---|
| Bryophyta | 1 | 32 |
| Bryophyta | 2 | 192 |
| Bryophyta | 3 | 139 |
| Bryophyta | 4 | 195 |
| Bryophyta | 5 | 137 |
| Bryophyta | 6 | 71 |
| Bryophyta | 7 | 27 |
| Marchantiophyta | 1 | 43 |
| Marchantiophyta | 2 | 97 |
| Marchantiophyta | 3 | 45 |
| Marchantiophyta | 4 | 36 |
| Marchantiophyta | 5 | 23 |
| Marchantiophyta | 6 | 8 |
| Marchantiophyta | 7 | 5 |
| phylum | ell_t | number of species |
|---|---|---|
| Bryophyta | 2 | 48 |
| Bryophyta | 3 | 269 |
| Bryophyta | 4 | 142 |
| Bryophyta | 5 | 155 |
| Bryophyta | 6 | 108 |
| Bryophyta | 7 | 58 |
| Bryophyta | 8 | 13 |
| Marchantiophyta | 2 | 27 |
| Marchantiophyta | 3 | 113 |
| Marchantiophyta | 4 | 51 |
| Marchantiophyta | 5 | 43 |
| Marchantiophyta | 6 | 13 |
| Marchantiophyta | 7 | 2 |
| Marchantiophyta | 8 | 8 |
Only remove substrate levels with less than 5 species (for Ellenberg variables this is not necessary because they are included as continuous covariate).
## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2
| phylum | substrate | n |
|---|---|---|
| Bryophyta | artificial stone | 84 |
| Bryophyta | decaying vegetation | 21 |
| Bryophyta | decorticated wood | 48 |
| Bryophyta | epiphytic on living wood | 73 |
| Bryophyta | gravel or sand | 106 |
| Bryophyta | mineral soil | 210 |
| Bryophyta | peat | 46 |
| Bryophyta | rock, hard | 95 |
| Bryophyta | rock, soft | 38 |
| Bryophyta | soil on rock | 68 |
| Marchantiophyta | artificial stone | 9 |
| Marchantiophyta | bryophyte | 17 |
| Marchantiophyta | decaying vegetation | 18 |
| Marchantiophyta | decorticated wood | 16 |
| Marchantiophyta | epiphytic on living wood | 15 |
| Marchantiophyta | gravel or sand | 34 |
| Marchantiophyta | mineral soil | 67 |
| Marchantiophyta | peat | 30 |
| Marchantiophyta | rock, hard | 14 |
| Marchantiophyta | rock, soft | 14 |
| Marchantiophyta | soil on rock | 20 |
## Warning: Ignoring unknown aesthetics: text## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: `group_by_()` is deprecated as of dplyr 0.7.0.
## Please use `group_by()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.## # A tibble: 124 x 2
## `n_hok_1980-1999` n
## <int> <int>
## 1 0 241
## 2 5 35
## 3 6 17
## 4 7 18
## 5 8 12
## 6 9 22
## 7 10 14
## 8 11 12
## 9 12 15
## 10 13 4
## # ... with 114 more rows## # A tibble: 145 x 2
## `n_hok_2000-2019` n
## <int> <int>
## 1 0 18
## 2 1 86
## 3 2 63
## 4 3 33
## 5 4 39
## 6 5 20
## 7 6 22
## 8 7 14
## 9 8 25
## 10 9 16
## # ... with 135 more rowsKeeping only species that occur in both periods (much improves model validation). (Alternative could be to include a factor with levels for lost, persisting, gained in the model to explain lost and gained species, but maybe see this as a separate model with the full dataset!)
Overdispersion (residual deviance divided by residual degrees of freedom >> 1)! Quasi-binomial model needed.
Should we include interaction between baseline proportion and substrate or ellenberg variables?
##
## Call:
## glm(formula = cbind(`n_hok_2000-2019` + 1, `n_hok_tot_2000-2019` -
## `n_hok_2000-2019` - 1) ~ qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) +
## phylum + qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum +
## (substrate + ell_l + ell_n + ell_f + ell_t) * phylum, family = "quasibinomial",
## data = analyse_data_telfer_agg)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -13.3930 -2.4523 -0.5277 1.7451 11.5813
##
## Coefficients: (1 not defined because of singularities)
## Estimate
## (Intercept) 0.581124
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) 0.932018
## phylumMarchantiophyta -0.436164
## substratebryophyte -0.234983
## substratedecaying vegetation 0.069042
## substratedecorticated wood 0.079133
## substrateepiphytic on living wood 0.440749
## substrategravel or sand -0.006071
## substratemineral soil -0.063548
## substratepeat 0.193737
## substraterock, hard 0.129607
## substraterock, soft 0.026071
## substratesoil on rock 0.043359
## ell_l -0.019053
## ell_n -0.029888
## ell_f -0.063934
## ell_t 0.041822
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.021463
## phylumMarchantiophyta:substratebryophyte NA
## phylumMarchantiophyta:substratedecaying vegetation -0.237880
## phylumMarchantiophyta:substratedecorticated wood -0.369963
## phylumMarchantiophyta:substrateepiphytic on living wood 0.233065
## phylumMarchantiophyta:substrategravel or sand -0.217055
## phylumMarchantiophyta:substratemineral soil -0.198928
## phylumMarchantiophyta:substratepeat -0.294218
## phylumMarchantiophyta:substraterock, hard -0.412046
## phylumMarchantiophyta:substraterock, soft -0.061837
## phylumMarchantiophyta:substratesoil on rock 0.053290
## phylumMarchantiophyta:ell_l -0.018365
## phylumMarchantiophyta:ell_n 0.021410
## phylumMarchantiophyta:ell_f -0.024859
## phylumMarchantiophyta:ell_t 0.101384
## Std. Error
## (Intercept) 0.207479
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) 0.020002
## phylumMarchantiophyta 0.498275
## substratebryophyte 0.355548
## substratedecaying vegetation 0.178141
## substratedecorticated wood 0.131272
## substrateepiphytic on living wood 0.119177
## substrategravel or sand 0.115150
## substratemineral soil 0.101872
## substratepeat 0.145852
## substraterock, hard 0.123034
## substraterock, soft 0.160941
## substratesoil on rock 0.125512
## ell_l 0.019759
## ell_n 0.022669
## ell_f 0.017658
## ell_t 0.023228
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.050436
## phylumMarchantiophyta:substratebryophyte NA
## phylumMarchantiophyta:substratedecaying vegetation 0.366808
## phylumMarchantiophyta:substratedecorticated wood 0.364577
## phylumMarchantiophyta:substrateepiphytic on living wood 0.385011
## phylumMarchantiophyta:substrategravel or sand 0.322868
## phylumMarchantiophyta:substratemineral soil 0.300539
## phylumMarchantiophyta:substratepeat 0.340603
## phylumMarchantiophyta:substraterock, hard 0.395109
## phylumMarchantiophyta:substraterock, soft 0.383068
## phylumMarchantiophyta:substratesoil on rock 0.335821
## phylumMarchantiophyta:ell_l 0.041151
## phylumMarchantiophyta:ell_n 0.052353
## phylumMarchantiophyta:ell_f 0.045773
## phylumMarchantiophyta:ell_t 0.053381
## t value
## (Intercept) 2.801
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) 46.596
## phylumMarchantiophyta -0.875
## substratebryophyte -0.661
## substratedecaying vegetation 0.388
## substratedecorticated wood 0.603
## substrateepiphytic on living wood 3.698
## substrategravel or sand -0.053
## substratemineral soil -0.624
## substratepeat 1.328
## substraterock, hard 1.053
## substraterock, soft 0.162
## substratesoil on rock 0.345
## ell_l -0.964
## ell_n -1.318
## ell_f -3.621
## ell_t 1.800
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.426
## phylumMarchantiophyta:substratebryophyte NA
## phylumMarchantiophyta:substratedecaying vegetation -0.649
## phylumMarchantiophyta:substratedecorticated wood -1.015
## phylumMarchantiophyta:substrateepiphytic on living wood 0.605
## phylumMarchantiophyta:substrategravel or sand -0.672
## phylumMarchantiophyta:substratemineral soil -0.662
## phylumMarchantiophyta:substratepeat -0.864
## phylumMarchantiophyta:substraterock, hard -1.043
## phylumMarchantiophyta:substraterock, soft -0.161
## phylumMarchantiophyta:substratesoil on rock 0.159
## phylumMarchantiophyta:ell_l -0.446
## phylumMarchantiophyta:ell_n 0.409
## phylumMarchantiophyta:ell_f -0.543
## phylumMarchantiophyta:ell_t 1.899
## Pr(>|t|)
## (Intercept) 0.005227
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) < 2e-16
## phylumMarchantiophyta 0.381663
## substratebryophyte 0.508877
## substratedecaying vegetation 0.698444
## substratedecorticated wood 0.546810
## substrateepiphytic on living wood 0.000233
## substrategravel or sand 0.957966
## substratemineral soil 0.532947
## substratepeat 0.184478
## substraterock, hard 0.292487
## substraterock, soft 0.871357
## substratesoil on rock 0.729846
## ell_l 0.335211
## ell_n 0.187753
## ell_f 0.000314
## ell_t 0.072183
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.670552
## phylumMarchantiophyta:substratebryophyte NA
## phylumMarchantiophyta:substratedecaying vegetation 0.516850
## phylumMarchantiophyta:substratedecorticated wood 0.310540
## phylumMarchantiophyta:substrateepiphytic on living wood 0.545130
## phylumMarchantiophyta:substrategravel or sand 0.501618
## phylumMarchantiophyta:substratemineral soil 0.508234
## phylumMarchantiophyta:substratepeat 0.387965
## phylumMarchantiophyta:substraterock, hard 0.297345
## phylumMarchantiophyta:substraterock, soft 0.871801
## phylumMarchantiophyta:substratesoil on rock 0.873960
## phylumMarchantiophyta:ell_l 0.655514
## phylumMarchantiophyta:ell_n 0.682692
## phylumMarchantiophyta:ell_f 0.587223
## phylumMarchantiophyta:ell_t 0.057912
##
## (Intercept) **
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) ***
## phylumMarchantiophyta
## substratebryophyte
## substratedecaying vegetation
## substratedecorticated wood
## substrateepiphytic on living wood ***
## substrategravel or sand
## substratemineral soil
## substratepeat
## substraterock, hard
## substraterock, soft
## substratesoil on rock
## ell_l
## ell_n
## ell_f ***
## ell_t .
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta
## phylumMarchantiophyta:substratebryophyte
## phylumMarchantiophyta:substratedecaying vegetation
## phylumMarchantiophyta:substratedecorticated wood
## phylumMarchantiophyta:substrateepiphytic on living wood
## phylumMarchantiophyta:substrategravel or sand
## phylumMarchantiophyta:substratemineral soil
## phylumMarchantiophyta:substratepeat
## phylumMarchantiophyta:substraterock, hard
## phylumMarchantiophyta:substraterock, soft
## phylumMarchantiophyta:substratesoil on rock
## phylumMarchantiophyta:ell_l
## phylumMarchantiophyta:ell_n
## phylumMarchantiophyta:ell_f
## phylumMarchantiophyta:ell_t .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for quasibinomial family taken to be 13.31708)
##
## Null deviance: 86097.7 on 783 degrees of freedom
## Residual deviance: 9531.1 on 753 degrees of freedom
## AIC: NA
##
## Number of Fisher Scoring iterations: 4## Analysis of Deviance Table
##
## Model: quasibinomial, link: logit
##
## Response: cbind(`n_hok_2000-2019` + 1, `n_hok_tot_2000-2019` - `n_hok_2000-2019` - 1)
##
## Terms added sequentially (first to last)
##
##
## Df Deviance
## NULL
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) 1 74063
## phylum 1 1075
## substrate 10 755
## ell_l 1 6
## ell_n 1 8
## ell_f 1 312
## ell_t 1 111
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum 1 10
## phylum:substrate 9 128
## phylum:ell_l 1 3
## phylum:ell_n 1 33
## phylum:ell_f 1 14
## phylum:ell_t 1 48
## Resid. Df
## NULL 783
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) 782
## phylum 781
## substrate 771
## ell_l 770
## ell_n 769
## ell_f 768
## ell_t 767
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum 766
## phylum:substrate 757
## phylum:ell_l 756
## phylum:ell_n 755
## phylum:ell_f 754
## phylum:ell_t 753
## Resid. Dev
## NULL 86098
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) 12035
## phylum 10959
## substrate 10205
## ell_l 10198
## ell_n 10191
## ell_f 9878
## ell_t 9767
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum 9757
## phylum:substrate 9630
## phylum:ell_l 9626
## phylum:ell_n 9593
## phylum:ell_f 9579
## phylum:ell_t 9531
## F
## NULL
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) 5561.5162
## phylum 80.7531
## substrate 5.6670
## ell_l 0.4553
## ell_n 0.5785
## ell_f 23.4477
## ell_t 8.3418
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum 0.7478
## phylum:substrate 1.0669
## phylum:ell_l 0.2609
## phylum:ell_n 2.4779
## phylum:ell_f 1.0325
## phylum:ell_t 3.6259
## Pr(>F)
## NULL
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) < 2.2e-16 ***
## phylum < 2.2e-16 ***
## substrate 3.258e-08 ***
## ell_l 0.500035
## ell_n 0.447137
## ell_f 1.558e-06 ***
## ell_t 0.003985 **
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum 0.387447
## phylum:substrate 0.385079
## phylum:ell_l 0.609654
## phylum:ell_n 0.115877
## phylum:ell_f 0.309902
## phylum:ell_t 0.057269 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Call:
## glm(formula = cbind(`n_hok_2000-2019`, `n_hok_tot_2000-2019` -
## `n_hok_2000-2019`) ~ qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) +
## phylum + qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum +
## substrate + phylum:substrate, family = "quasibinomial", data = analyse_data_telfer_agg)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -13.4252 -2.4596 -0.4555 1.8609 13.7597
##
## Coefficients: (1 not defined because of singularities)
## Estimate
## (Intercept) 0.19747
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) 0.93289
## phylumMarchantiophyta -0.19266
## substratebryophyte -0.44616
## substratedecaying vegetation 0.02417
## substratedecorticated wood 0.05016
## substrateepiphytic on living wood 0.47077
## substrategravel or sand -0.03462
## substratemineral soil -0.11935
## substratepeat 0.08668
## substraterock, hard 0.12204
## substraterock, soft 0.10029
## substratesoil on rock 0.09399
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.04230
## phylumMarchantiophyta:substratebryophyte NA
## phylumMarchantiophyta:substratedecaying vegetation -0.32723
## phylumMarchantiophyta:substratedecorticated wood -0.41701
## phylumMarchantiophyta:substrateepiphytic on living wood 0.18268
## phylumMarchantiophyta:substrategravel or sand -0.35145
## phylumMarchantiophyta:substratemineral soil -0.21636
## phylumMarchantiophyta:substratepeat -0.33846
## phylumMarchantiophyta:substraterock, hard -0.34373
## phylumMarchantiophyta:substraterock, soft -0.22809
## phylumMarchantiophyta:substratesoil on rock -0.04555
## Std. Error
## (Intercept) 0.09194
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) 0.01993
## phylumMarchantiophyta 0.28953
## substratebryophyte 0.35083
## substratedecaying vegetation 0.18147
## substratedecorticated wood 0.13395
## substrateepiphytic on living wood 0.12532
## substrategravel or sand 0.11758
## substratemineral soil 0.10484
## substratepeat 0.13659
## substraterock, hard 0.12973
## substraterock, soft 0.17017
## substratesoil on rock 0.13238
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.04841
## phylumMarchantiophyta:substratebryophyte NA
## phylumMarchantiophyta:substratedecaying vegetation 0.37080
## phylumMarchantiophyta:substratedecorticated wood 0.37424
## phylumMarchantiophyta:substrateepiphytic on living wood 0.37980
## phylumMarchantiophyta:substrategravel or sand 0.32816
## phylumMarchantiophyta:substratemineral soil 0.31053
## phylumMarchantiophyta:substratepeat 0.33750
## phylumMarchantiophyta:substraterock, hard 0.42152
## phylumMarchantiophyta:substraterock, soft 0.40514
## phylumMarchantiophyta:substratesoil on rock 0.35294
## t value
## (Intercept) 2.148
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) 46.818
## phylumMarchantiophyta -0.665
## substratebryophyte -1.272
## substratedecaying vegetation 0.133
## substratedecorticated wood 0.374
## substrateepiphytic on living wood 3.757
## substrategravel or sand -0.294
## substratemineral soil -1.138
## substratepeat 0.635
## substraterock, hard 0.941
## substraterock, soft 0.589
## substratesoil on rock 0.710
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.874
## phylumMarchantiophyta:substratebryophyte NA
## phylumMarchantiophyta:substratedecaying vegetation -0.883
## phylumMarchantiophyta:substratedecorticated wood -1.114
## phylumMarchantiophyta:substrateepiphytic on living wood 0.481
## phylumMarchantiophyta:substrategravel or sand -1.071
## phylumMarchantiophyta:substratemineral soil -0.697
## phylumMarchantiophyta:substratepeat -1.003
## phylumMarchantiophyta:substraterock, hard -0.815
## phylumMarchantiophyta:substraterock, soft -0.563
## phylumMarchantiophyta:substratesoil on rock -0.129
## Pr(>|t|)
## (Intercept) 0.032033
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) < 2e-16
## phylumMarchantiophyta 0.505987
## substratebryophyte 0.203850
## substratedecaying vegetation 0.894061
## substratedecorticated wood 0.708168
## substrateepiphytic on living wood 0.000185
## substrategravel or sand 0.768513
## substratemineral soil 0.255308
## substratepeat 0.525886
## substraterock, hard 0.347167
## substraterock, soft 0.555790
## substratesoil on rock 0.477928
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.382446
## phylumMarchantiophyta:substratebryophyte NA
## phylumMarchantiophyta:substratedecaying vegetation 0.377784
## phylumMarchantiophyta:substratedecorticated wood 0.265508
## phylumMarchantiophyta:substrateepiphytic on living wood 0.630664
## phylumMarchantiophyta:substrategravel or sand 0.284517
## phylumMarchantiophyta:substratemineral soil 0.486174
## phylumMarchantiophyta:substratepeat 0.316251
## phylumMarchantiophyta:substraterock, hard 0.415071
## phylumMarchantiophyta:substraterock, soft 0.573601
## phylumMarchantiophyta:substratesoil on rock 0.897348
##
## (Intercept) *
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) ***
## phylumMarchantiophyta
## substratebryophyte
## substratedecaying vegetation
## substratedecorticated wood
## substrateepiphytic on living wood ***
## substrategravel or sand
## substratemineral soil
## substratepeat
## substraterock, hard
## substraterock, soft
## substratesoil on rock
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta
## phylumMarchantiophyta:substratebryophyte
## phylumMarchantiophyta:substratedecaying vegetation
## phylumMarchantiophyta:substratedecorticated wood
## phylumMarchantiophyta:substrateepiphytic on living wood
## phylumMarchantiophyta:substrategravel or sand
## phylumMarchantiophyta:substratemineral soil
## phylumMarchantiophyta:substratepeat
## phylumMarchantiophyta:substraterock, hard
## phylumMarchantiophyta:substraterock, soft
## phylumMarchantiophyta:substratesoil on rock
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for quasibinomial family taken to be 14.77914)
##
## Null deviance: 86541 on 783 degrees of freedom
## Residual deviance: 10259 on 761 degrees of freedom
## AIC: NA
##
## Number of Fisher Scoring iterations: 4## Analysis of Deviance Table
##
## Model: quasibinomial, link: logit
##
## Response: cbind(`n_hok_2000-2019`, `n_hok_tot_2000-2019` - `n_hok_2000-2019`)
##
## Terms added sequentially (first to last)
##
##
## Df Deviance Resid. Df
## NULL 783
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) 1 74320 782
## phylum 1 1092 781
## substrate 10 764 771
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum 1 15 770
## phylum:substrate 9 90 761
## Resid. Dev F
## NULL 86541
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) 12221 5028.7428
## phylum 11128 73.9045
## substrate 10364 5.1726
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum 10349 0.9934
## phylum:substrate 10259 0.6787
## Pr(>F)
## NULL
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) < 2.2e-16 ***
## phylum < 2.2e-16 ***
## substrate 2.346e-07 ***
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum 0.3192
## phylum:substrate 0.7287
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Call:
## glm(formula = cbind(`n_hok_2000-2019`, `n_hok_tot_2000-2019` -
## `n_hok_2000-2019`) ~ qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) +
## phylum + qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum +
## (ell_l + ell_n + ell_f + ell_t) * phylum, family = "quasibinomial",
## data = analyse_data_telfer_agg)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -9.824 -2.563 -0.525 1.712 14.203
##
## Coefficients:
## Estimate
## (Intercept) 0.829980
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) 0.922411
## phylumMarchantiophyta -0.364332
## ell_l -0.036997
## ell_n -0.027142
## ell_f -0.077162
## ell_t 0.036164
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.043151
## phylumMarchantiophyta:ell_l -0.001829
## phylumMarchantiophyta:ell_n 0.066577
## phylumMarchantiophyta:ell_f -0.070417
## phylumMarchantiophyta:ell_t 0.062708
## Std. Error
## (Intercept) 0.184957
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) 0.019297
## phylumMarchantiophyta 0.374915
## ell_l 0.018191
## ell_n 0.021461
## ell_f 0.016998
## ell_t 0.023175
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.050779
## phylumMarchantiophyta:ell_l 0.038826
## phylumMarchantiophyta:ell_n 0.047973
## phylumMarchantiophyta:ell_f 0.041641
## phylumMarchantiophyta:ell_t 0.052088
## t value
## (Intercept) 4.487
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) 47.800
## phylumMarchantiophyta -0.972
## ell_l -2.034
## ell_n -1.265
## ell_f -4.540
## ell_t 1.560
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.850
## phylumMarchantiophyta:ell_l -0.047
## phylumMarchantiophyta:ell_n 1.388
## phylumMarchantiophyta:ell_f -1.691
## phylumMarchantiophyta:ell_t 1.204
## Pr(>|t|)
## (Intercept) 8.31e-06
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) < 2e-16
## phylumMarchantiophyta 0.3315
## ell_l 0.0423
## ell_n 0.2064
## ell_f 6.54e-06
## ell_t 0.1191
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.3957
## phylumMarchantiophyta:ell_l 0.9624
## phylumMarchantiophyta:ell_n 0.1656
## phylumMarchantiophyta:ell_f 0.0912
## phylumMarchantiophyta:ell_t 0.2290
##
## (Intercept) ***
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) ***
## phylumMarchantiophyta
## ell_l *
## ell_n
## ell_f ***
## ell_t
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta
## phylumMarchantiophyta:ell_l
## phylumMarchantiophyta:ell_n
## phylumMarchantiophyta:ell_f .
## phylumMarchantiophyta:ell_t
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for quasibinomial family taken to be 13.90762)
##
## Null deviance: 86541 on 783 degrees of freedom
## Residual deviance: 10273 on 772 degrees of freedom
## AIC: NA
##
## Number of Fisher Scoring iterations: 4Models including substrate are rank-deficient and the fit may be misleading…
## Warning in predict.lm(object, newdata, se.fit, scale = residual.scale, type = if
## (type == : prediction from a rank-deficient fit may be misleading
Same figure but this time in link-scale (to obtain Telfer-like figures):
## Warning in predict.lm(object, newdata, se.fit, scale = residual.scale, type = if
## (type == : prediction from a rank-deficient fit may be misleading
## Warning in predict.lm(object, newdata, se.fit, scale = residual.scale, type = if
## (type == : prediction from a rank-deficient fit may be misleading
